rs3748391

Variant names:

• chr16-87255411-T-A
• rs3748391
• ENST00000562840.1:n.110+47242A>T

Your query was ambiguous. Multiple possible variants found:

• chr16-87255411-T-A
• chr16-87255411-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000562840.1(C16orf95):​n.110+47242A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 151,888 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0012 (1 hom., cov: 31)
• Consequence: C16orf95 ENST00000562840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972
• Publications: 11 publications found

Genes affected

C16orf95 (HGNC:40033): (chromosome 16 open reading frame 95)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C16orf95	ENST00000562840.1	n.110+47242A>T		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.00115 AC: 175 AN: 151770 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000460

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00348

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000663

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00132

Gnomad OTH AF: 0.00288

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00115 AC: 175 AN: 151888 Hom.: 1 Cov.: 31 AF XY: 0.00121 AC XY: 90 AN XY: 74246

African (AFR) AF: 0.000459 AC: 19 AN: 41414

American (AMR) AF: 0.00348 AC: 53 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5148

South Asian (SAS) AF: 0.00 AC: 0 AN: 4806

European-Finnish (FIN) AF: 0.000663 AC: 7 AN: 10564

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.00132 AC: 90 AN: 67934

Other (OTH) AF: 0.00285 AC: 6 AN: 2104

Alfa AF: 0.00 Hom.: 65235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.59
DANN	Benign	0.15
PhyloP100		-0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3748391; hg19: chr16-87289017;